Variant report

Variant	rs2336448
Chromosome Location	chr12:50212628-50212629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50210017..50215332-chr12:50220398..50225792,6	MCF-7	breast:
2	chr12:50210959..50213852-chr12:50216092..50218529,3	K562	blood:
3	chr12:50200354..50204251-chr12:50212561..50215291,3	K562	blood:

Variant related genes	Relation type
ENSG00000258057	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1075366	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1077498	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1077499	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10783320	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875969	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875970	0.81[EUR][1000 genomes]
rs11169161	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169162	0.81[EUR][1000 genomes]
rs11169167	0.84[AFR][1000 genomes]
rs11615911	0.81[EUR][1000 genomes]
rs1470909	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290442	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2603104	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2603107	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2603110	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2603111	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2720291	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2720296	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2720298	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2954129	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4463912	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4488285	0.81[EUR][1000 genomes]
rs4898530	0.96[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59766494	0.81[EUR][1000 genomes]
rs60062868	0.81[EUR][1000 genomes]
rs729281	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7313400	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7313563	0.81[CEU][hapmap]
rs7488361	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977112	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
2	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:50189200-50214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:50193800-50214600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:50195200-50218400	Weak transcription	K562	blood
6	chr12:50195800-50214400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:50197600-50220400	Weak transcription	A549	lung
8	chr12:50199400-50218400	Weak transcription	HMEC	breast
9	chr12:50199600-50214600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:50199600-50214800	Weak transcription	Liver	Liver
11	chr12:50200000-50213800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:50200000-50214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:50200000-50214600	Weak transcription	Pancreas	Pancrea
14	chr12:50200000-50216800	Weak transcription	NHEK	skin
15	chr12:50200000-50219400	Weak transcription	Gastric	stomach
16	chr12:50200200-50214800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:50200400-50214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:50200400-50215000	Weak transcription	Dnd41	blood
19	chr12:50202200-50217000	Weak transcription	HepG2	liver
20	chr12:50202200-50218400	Weak transcription	Fetal Brain Female	brain
21	chr12:50203000-50214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:50203600-50218000	Weak transcription	NH-A	brain
23	chr12:50203600-50219800	Weak transcription	Aorta	Aorta
24	chr12:50203800-50213600	Weak transcription	NHDF-Ad	bronchial
25	chr12:50203800-50214600	Weak transcription	Osteobl	bone
26	chr12:50203800-50215400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:50203800-50217800	Weak transcription	NHLF	lung
28	chr12:50203800-50218600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:50204200-50217800	Weak transcription	Fetal Brain Male	brain
30	chr12:50204400-50213200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:50204400-50213600	Weak transcription	HUVEC	blood vessel
32	chr12:50204400-50213800	Weak transcription	Brain Anterior Caudate	brain
33	chr12:50204400-50214600	Weak transcription	Fetal Intestine Small	intestine
34	chr12:50204400-50216600	Weak transcription	Brain Germinal Matrix	brain
35	chr12:50204400-50220200	Weak transcription	Fetal Kidney	kidney
36	chr12:50205000-50214600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:50205000-50214600	Weak transcription	Brain Angular Gyrus	brain
38	chr12:50205000-50215000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:50205000-50215200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:50205200-50213600	Weak transcription	Right Ventricle	heart
41	chr12:50205200-50213600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:50205200-50213600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:50205200-50213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:50205200-50214400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:50205200-50214600	Weak transcription	Lung	lung
46	chr12:50205200-50215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:50205200-50215200	Weak transcription	Fetal Lung	lung
48	chr12:50205200-50219000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:50205200-50220000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:50205400-50214200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links